Prendergast has written extensively on Africa and is the author or co-author of eleven books. His latest book is Congo Stories: Battling Five Centuries of Exploitation and Greed (2018), co-authored with Congolese activist Fidel Bafilemba and featuring photographs by Ryan Gosling He is currently working on a project concerning the Democratic Republic of the Congo with Gosling and New Yorker writer Kelefa Sanneh.[15]

Prendergast appeared the documentaries Sand and Sorrow, Darfur Now, 3 Points,[24] and War Child.[25] He co-produced Journey Into Sunset,[26] and is Executive Producer of Staging Hope: Acts of Peace in Northern Uganda,[27] both about Northern Uganda.

Jane Bussmann was inspired by his work and meetings with him to write her 2012 book The Worst Date Ever: or How it Took a Comedy Writer to Expose Joseph Kony and Africa's Secret War,[28] a comic/tragic story of her attempt as a novice foreign correspondent to expose the truth about the war in Uganda.

Peace, Development, and People of the Horn of Africa, by John Prendergast, Bread for the World (Organization). Institute on Hunger & Development, Center of Concern (Washington, D.C.), published by Center of Concern, 1992 ISBN978-0-9628058-2-0

Civilian Devastation: Abuses by All Parties in the War in Southern Sudan, by Jemera Rone, John Prendergast, Karen Sorensen, Human Rights Watch/Africa, Human Rights Watch (Organization), published by Human Rights Watch, 1994 ISBN978-1-56432-129-9

Without Troops & Tanks: The Emergency Relief Desk and the Cross Border Operation into Eritrea and Tigray, by Mark R. Duffield, John Prendergast, published by The Red Sea Press, 1994 ISBN978-1-56902-003-6